I live in the AOR and travel between Kuwait, Iraq, and Afghanistan. I spend most of my time in Afghanistan.
The apple international adapter kit for the power supplies is great. It has every plug you'll ever need for traveling.
There are several DOD Acronym applications that are useful for quickly looking up a new acronym (the military loves their acronyms).
There are several good news apps that help stay on top of what's happening in CONUS. Thompson Reuters, and the new abc news app are great. A RSS reader like Early Edition helps stay on top of your RSS feeds, again saving time browsing the web when connection speeds are slow.
Zinio is great for magazine subscriptions.
The Kindle and iBook application are great for passing spare time. I also use the iBook application to store and read PDF files sent to me by e-mail. It's great for watching movies or TV shows, but you'll need a PC to sync them over to it, you'll not have much luck downloading movies and TV shows at most locations in Iraq or Afghanistan due to network speeds.
Handbrake for the Mac is a great tool for converting inexpensive locally purchase movies and TV Shows to a format that can be synced with your iPad.
In Afghanistan, you can use Roshan for data. First purchase a Roshan sim card and a $55 recharge card. Write down the phone number! Put the Roshan card in a cell phone, add the minutes from the recharge card, and send a text message to 167 with the body "GPRS on". You may or may not get a reply (should be OK either way). I'd send it a couple times to be sure. Take the sim out of the cell phone and cut it down using your AT&T micro sim that came with the iPad as a format. Put it in your iPad. Go to "Settings", then select "Cellular Data" from the left. Make sure Cellular Data and Roaming are turned on. Select "APN Settings". Your APN is "internet". Leave the user name and password blank. That's it. It is very slow, but will allow for e-mail and basic web browsing or chat with family (I use IM+ for chat and am very happy with it). I'd use your computer or wifi to download anything large like apps, movies, music, etc to save money. To recharge, just go to your phone store on base, and instead of buying recharge cards, ask them to transfer minutes from their phone to yours using the number of your sim card. I've used Roshan at Bagram and Kabul with no issues and it works most of the time in Kandahar.
In Kuwait, I've used both Zain and Viva successfully with the iPad. Both now sell micro sims. Wataniya has micro sims and should work, but I havent tried them. Both Watania and Zain offer pre-paid (no contract) and post paid data plans.
I use the standard apple case. A lot of people don't like it. It isn't pretty, but it is brilliant in its simplicity and keeps everything protected and still nice and slim. I'm planning to get an Otterbox case for those times when I travel to harsher locations or fly MILAIR and/or convoy.